WebDriverAgent has a concept of application under test similar to what’s described in GitHub - appium/appium-mac2-driver: Next-gen Appium macOS driver, backed by Apple XCTest
In order to avoid the above exception to be thrown the application under test must be explicitly terminated by appium-xcuitest-driver/docs/reference/execute-methods.md at master · appium/appium-xcuitest-driver · GitHub
The above API must also be called explicitly even if the app was closed in some other way to notify WDA about the application state change.